inst/tinytest/test_gDataMPP.R

In statgenMPP: QTL Mapping for Multi Parent Populations

### Test gDataMPP

## Define input files.

markerFiles <- c(system.file("extdata/multipop", "AxB.txt",
                             package = "statgenMPP"),
                 system.file("extdata/multipop", "AxC.txt",
                             package = "statgenMPP"))
mapFile <- system.file("extdata/multipop", "mapfile.txt",
                       package = "statgenMPP")

pheno <- read.delim(system.file("extdata/multipop", "AxBxCpheno.txt",
                                package = "statgenMPP"))

## Compute IBD probabilities.
ABC <- calcIBDMPP(crossNames = c("AxB", "AxC"),
                  markerFiles = markerFiles,
                  pheno = pheno, popType = "F4DH",
                  mapFile = mapFile, evalDist = 5)

## Check summary.

sumABC <- summary(ABC)

expect_inherits(sumABC, "summary.gDataMPP")
expect_equal(names(sumABC), c("mapSum", "markerSum", "phenoSum", "covarSum"))

## Check printed output.
sumABCprnt <- capture.output(summary(ABC))
expect_true("\tNumber of traits: 1 " %in% sumABCprnt)
expect_true("\tTraitnames: yield " %in% sumABCprnt)
expect_true(" AxB:100  " %in% sumABCprnt)
expect_true(" AxC: 80  " %in% sumABCprnt)

# Function is a copy of function from statgenGWAS except for markerSum bit.
# Only check that.

expect_inherits(sumABC$markerSum, "list")
expect_equal(names(sumABC$markerSum), c("nMarkers", "nGeno", "markerContent"))
expect_equal(sumABC$markerSum$markerContent, c(`parents:` = "A, B, C"))

## Check plot.

# All plots are called directly from statgenGWAS or statgenIBD.
# Not much can be tested here.

# genMap
expect_error(plot(ABC, highlight = "EXT_3_31"),
             "The following highlight markers are not in map")
expect_silent(p1 <- plot(ABC, plotType = "genMap"))
p1a <- plot(ABC, highlight = "EXT_3_30")

expect_equal(length(p1a$layers), length(p1$layers) + 2)


expect_silent(p2 <- plot(ABC, plotType = "singleGeno", genotype = "AxB0001"))
expect_silent(p3 <- plot(ABC, plotType = "allGeno"))
expect_silent(p4 <- plot(ABC, plotType = "pedigree"))